Fixes #2596

Open-Systems-Pharmacology · May 5, 2023 · bf6aa8e · bf6aa8e
1 parent 98555fa
commit bf6aa8e
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Showing 29 changed files with 200 additions and 191 deletions.
diff --git a/src/PKSim.Assets.Images/PKSim.Assets.Images.csproj b/src/PKSim.Assets.Images/PKSim.Assets.Images.csproj
@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-hTRUM" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.0-hTRUM" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.177" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.177" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.Assets/PKSim.Assets.csproj b/src/PKSim.Assets/PKSim.Assets.csproj
@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-hTRUM" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.0-hTRUM" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.177" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.177" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.BatchTool/PKSim.BatchTool.csproj b/src/PKSim.BatchTool/PKSim.BatchTool.csproj
@@ -59,8 +59,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="12.0.0-hTRUM" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-hTRUM" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.177" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.177" />
     <PackageReference Include="OSPSuite.DevExpress" Version="21.2.3" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />

diff --git a/src/PKSim.CLI.Core/PKSim.CLI.Core.csproj b/src/PKSim.CLI.Core/PKSim.CLI.Core.csproj
@@ -27,9 +27,9 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-hTRUM" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.177" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.0-hTRUM" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.177" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.CLI/PKSim.CLI.csproj b/src/PKSim.CLI/PKSim.CLI.csproj
@@ -61,9 +61,9 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.8.0" />
     <PackageReference Include="Microsoft.Extensions.Logging.Console" Version="3.1.0" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.0-hTRUM" />
-    <PackageReference Include="OSPSuite.Presentation" Version="12.0.0-hTRUM" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-hTRUM" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.177" />
+    <PackageReference Include="OSPSuite.Presentation" Version="12.0.177" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.177" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />

diff --git a/src/PKSim.Core/Mappers/IndividualToPopulationSettingsMapper.cs b/src/PKSim.Core/Mappers/IndividualToPopulationSettingsMapper.cs
@@ -70,7 +70,7 @@ public RandomPopulationSettings MapFrom(Individual individual)
       private bool shouldVaryInPopulation(OriginDataParameter originDataParameter)
       {
          //here list all discrete parameters that cannot be varied
-         return !originDataParameter.NameIsOneOf(HIDiseaseStateImplementation.CHILD_PUGH_SCORE);
+         return !originDataParameter.NameIsOneOf(CHILD_PUGH_SCORE);
       }
 
       private ParameterRange constrainedParameterRangeFrom(IParameter parameter)

diff --git a/src/PKSim.Core/Mappers/ParameterListOfValuesRetriever.cs b/src/PKSim.Core/Mappers/ParameterListOfValuesRetriever.cs
@@ -33,8 +33,6 @@ public ParameterListOfValuesRetriever() : this(new HashSet<string>(AllWithListOf
       public ParameterListOfValuesRetriever(HashSet<string> parameterWithListOfValues)
       {
          _parameterWithListOfValues = parameterWithListOfValues;
-         //TODO MOVE TO CORE
-         _parameterWithListOfValues.Add(HIDiseaseStateImplementation.CHILD_PUGH_SCORE);
          _formatter = new NumericFormatter<double>(NumericFormatterOptions.Instance);
       }
 
@@ -110,7 +108,7 @@ public void UpdateLisOfValues(ICache<double, string> listOfValues, IWithName par
             listOfValues.Add(SINK_CONDITION, SinkCondition);
             listOfValues.Add(NO_SINK_CONDITION, NoSinkCondition);
          }
-         else if (parameter.IsNamed(HIDiseaseStateImplementation.CHILD_PUGH_SCORE))
+         else if (parameter.IsNamed(CHILD_PUGH_SCORE))
          {
             listOfValues.Add(HIDiseaseStateImplementation.ChildPughScore.A, ChildPughScoreFor("A"));
             listOfValues.Add(HIDiseaseStateImplementation.ChildPughScore.B, ChildPughScoreFor("B"));

diff --git a/src/PKSim.Core/PKSim.Core.csproj b/src/PKSim.Core/PKSim.Core.csproj
@@ -31,10 +31,10 @@
   <ItemGroup>
     <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.0-hTRUM" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.0-hTRUM" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.0-hTRUM" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.0-hTRUM" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.177" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.177" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.177" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.177" />
     <PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
   </ItemGroup>
 

diff --git a/src/PKSim.Core/Services/CKDDiseaseStateImplementation.cs b/src/PKSim.Core/Services/CKDDiseaseStateImplementation.cs
@@ -22,7 +22,6 @@ private enum CKDStage
          Stage5,
       }
 
-      private readonly IValueOriginRepository _valueOriginRepository;
       private readonly IDimension _dimensionForGFR;
       public const string TARGET_GFR = "eGFR";
       private readonly IDimension _ageDimension;
@@ -37,7 +36,6 @@ public CKDDiseaseStateImplementation(
          IContainerTask containerTask,
          IParameterSetUpdater parameterSetUpdater) : base(valueOriginRepository, formulaFactory, individualFactory, containerTask, parameterSetUpdater, CoreConstants.DiseaseStates.CKD)
       {
-         _valueOriginRepository = valueOriginRepository;
          _dimensionForGFR = dimensionRepository.DimensionForUnit(GFR_UNIT);
          _ageDimension = dimensionRepository.AgeInYears;
       }
@@ -74,7 +72,7 @@ IParameter gastricEmptyingTime
 
       public override bool ApplyForPopulationTo(Individual individual) => applyTo(individual, UpdateParameterValue);
 
-      private bool applyTo(Individual individual, Action<IParameter, double, bool> updateParameterFunc)
+      private bool applyTo(Individual individual, Action<ParameterUpdate> updateParameterFunc)
       {
          var targetGFR = individual.OriginData.DiseaseStateParameters.FindByName(TARGET_GFR);
 
@@ -93,26 +91,26 @@ private bool applyTo(Individual individual, Action<IParameter, double, bool> upd
 
          //Adjust kidney volume and update fat accordingly
          var healthyKidneyVolume = kidneyVolume.Value;
-         updateParameterFunc(kidneyVolume, getKidneyVolumeFactor(targetGFRValue) / getKidneyVolumeFactor(GFR_0), true);
-         updateParameterFunc(fatVolume, fatVolume.Value + healthyKidneyVolume - kidneyVolume.Value, false);
+         updateParameterFunc(new(kidneyVolume, getKidneyVolumeFactor(targetGFRValue) / getKidneyVolumeFactor(GFR_0)));
+         updateParameterFunc(new(fatVolume, fatVolume.Value + healthyKidneyVolume - kidneyVolume.Value, ParameterUpdateMode.Value));
 
          //Adjust renal blood flow spec
-         updateParameterFunc(kidneySpecificBloodFlowRate, getRenalBloodFlowFactor(targetGFRValue) / getRenalBloodFlowFactor(GFR_0), true);
+         updateParameterFunc(new(kidneySpecificBloodFlowRate, getRenalBloodFlowFactor(targetGFRValue) / getRenalBloodFlowFactor(GFR_0)));
 
          //Correct specific GFR
-         updateParameterFunc(GFR_Spec, targetGFRValue / GFR_0 * healthyKidneyVolume / kidneyVolume.Value, true);
+         updateParameterFunc(new(GFR_Spec, targetGFRValue / GFR_0 * healthyKidneyVolume / kidneyVolume.Value));
 
          var (plasmaProteinScaleFactor, gastricEmptyingTimeFactor, smallIntestinalTransitTimeFactor) = getCategorialFactors(targetGFRValue);
 
          //Categorial Parameters as constant: We set the value as is as the value will not be reset when creating a population
-         updateParameterFunc(plasmaProteinScaleFactorParameter, plasmaProteinScaleFactor, false);
+         updateParameterFunc(new(plasmaProteinScaleFactorParameter, plasmaProteinScaleFactor, ParameterUpdateMode.Value));
 
          //Categorial Parameters distributed: We apply the variation to the default value
-         updateParameterFunc(gastricEmptyingTime, gastricEmptyingTimeFactor, true);
-         updateParameterFunc(smallIntestinalTransitTime, smallIntestinalTransitTimeFactor, true);
+         updateParameterFunc(new(gastricEmptyingTime, gastricEmptyingTimeFactor));
+         updateParameterFunc(new(smallIntestinalTransitTime, smallIntestinalTransitTimeFactor));
 
          //Special case for Hematocrit
-         updateParameterFunc(hct, getHematocritFactor(targetGFRValue, individual.OriginData.Gender), true);
+         updateParameterFunc(new(hct, getHematocritFactor(targetGFRValue, individual.OriginData.Gender)));
 
          return true;
       }
@@ -156,13 +154,6 @@ private double getHematocritFactor(double targetGFR, Gender gender)
          return diseaseValue / healthyValue;
       }
 
-      private void updateValueOriginsFor(IParameter parameter)
-      {
-         parameter.ValueOrigin.UpdateAllFrom(_valueOriginRepository.FindBy(CKD_VALUE_ORIGIN_ID));
-         //Make sure we mark this parameter as changed by create individual. It might already be the case but in that case, it does not change anything
-         parameter.IsChangedByCreateIndividual = true;
-      }
-
       private double getKidneyVolumeFactor(double gfrValue) => getFactor(gfrValue, -6.3E-5, 0.0149, 4.13);
 
       private double getRenalBloodFlowFactor(double gfrValue) => getFactor(gfrValue, -3.1E-5, 0.0170, 4.09);

diff --git a/src/PKSim.Core/Services/HIDiseaseStateImplementation.cs b/src/PKSim.Core/Services/HIDiseaseStateImplementation.cs
@@ -66,8 +66,6 @@ private static HIFactors createFactors(double forA, double forB, double forC) =>
          {"CYP2D6", createFactors(0.76, 0.33, 0.11)},
       };
 
-      public const string CHILD_PUGH_SCORE = "Child-Pugh score";
-
       private const int HI_EDGINTON_VALUE_ORIGIN_ID = 93;
       private const int HI_JOHNSON_VALUE_ORIGIN_ID = 94;
 
@@ -89,7 +87,7 @@ public HIDiseaseStateImplementation(IDimensionRepository dimensionRepository,
 
       public override bool ApplyForPopulationTo(Individual individual) => applyTo(individual, UpdateParameterValue);
 
-      private bool applyTo(Individual individual, Action<IParameter, double, bool> updateParameterFunc)
+      private bool applyTo(Individual individual, Action<ParameterUpdate> updateParameterFunc)
       {
          updateBloodFlows(individual, updateParameterFunc);
          updateVolumes(individual, updateParameterFunc);
@@ -129,45 +127,45 @@ protected override IReadOnlyList<IParameter> ParameterChangedByDiseaseStateAsLis
          var kidney = organism.Organ(KIDNEY);
          var liver = organism.Organ(LIVER);
 
-         var organsBloodFlow = new[] {STOMACH, SMALL_INTESTINE, LARGE_INTESTINE, SPLEEN, PANCREAS, LIVER, KIDNEY, BONE, FAT, GONADS, HEART, MUSCLE, SKIN};
+         //Oddly enough the brain blood flow is unaffected within hepatic disease, largely due to compensatory mechanisms from some of the decreased blood flow to other organs.
+         var organsBloodFlow = new[] { BONE, FAT, GONADS, HEART, KIDNEY, LIVER, MUSCLE, PANCREAS, LARGE_INTESTINE, SKIN, SMALL_INTESTINE, SPLEEN, STOMACH};
          var bloodFlows = organsBloodFlow.Select(x => organism.Organ(x).Parameter(SPECIFIC_BLOOD_FLOW_RATE)).ToList();
 
          return new[]
          {
             organism.Parameter(HCT),
             organism.Parameter(CHILD_PUGH_SCORE),
-            organism.Parameter(CHILD_PUGH_SCORE),
             organism.Parameter(ONTOGENY_FACTOR_ALBUMIN),
             organism.Parameter(ONTOGENY_FACTOR_AGP),
             kidney.Parameter(GFR_SPEC),
             liver.Parameter(VOLUME),
          }.Union(bloodFlows).ToList();
       }
 
-      private void updateOntogenyFactory(Individual individual, Action<IParameter, double, bool> updateParameterFunc)
+      private void updateOntogenyFactory(Individual individual, Action<ParameterUpdate> updateParameterFunc)
       {
          var score = childPughScoreFor(individual);
          var organism = individual.Organism;
-         updateParameterFunc(organism.Parameter(ONTOGENY_FACTOR_ALBUMIN), _albuminFactor[score], true);
-         updateParameterFunc(organism.Parameter(ONTOGENY_FACTOR_AGP), _agpFactor[score], true);
+         updateParameterFunc(new(organism.Parameter(ONTOGENY_FACTOR_ALBUMIN), _albuminFactor[score]));
+         updateParameterFunc(new(organism.Parameter(ONTOGENY_FACTOR_AGP), _agpFactor[score]));
       }
 
-      private void updateGFR(Individual individual, Action<IParameter, double, bool> updateParameterFunc)
+      private void updateGFR(Individual individual, Action<ParameterUpdate> updateParameterFunc)
       {
          var score = childPughScoreFor(individual);
          var kidney = individual.Organism.Organ(KIDNEY);
          var GFR_spec = kidney.Parameter(GFR_SPEC);
-         updateParameterFunc(GFR_spec, _gfrScalingFactor[score], true);
+         updateParameterFunc(new(GFR_spec, _gfrScalingFactor[score]));
       }
 
-      private void updateHematocrit(Individual individual, Action<IParameter, double, bool> updateParameterFunc)
+      private void updateHematocrit(Individual individual, Action<ParameterUpdate> updateParameterFunc)
       {
          var score = childPughScoreFor(individual);
          var hct = individual.Organism.Parameter(HCT);
-         updateParameterFunc(hct, _hematocritScalingFactor[score], true);
+         updateParameterFunc(new(hct, _hematocritScalingFactor[score]));
       }
 
-      private void updateBloodFlows(Individual individual, Action<IParameter, double, bool> updateParameterFunc)
+      private void updateBloodFlows(Individual individual, Action<ParameterUpdate> updateParameterFunc)
       {
          var score = childPughScoreFor(individual);
          var organism = individual.Organism;
@@ -188,24 +186,24 @@ private void updateBloodFlows(Individual individual, Action<IParameter, double,
          otherOrgans.Each(x => updateBloodFlow(x, _otherOrgansFlowScalingFactor[score]));
       }
 
-      private void updateVolumes(Individual individual, Action<IParameter, double, bool> updateParameterFunc)
+      private void updateVolumes(Individual individual, Action<ParameterUpdate> updateParameterFunc)
       {
          var score = childPughScoreFor(individual);
          var organism = individual.Organism;
          var parameter = organism.Container(LIVER).Parameter(VOLUME);
-         updateParameterFunc(parameter, _hepaticVolumeScalingFactor[score], true);
+         updateParameterFunc(new(parameter, _hepaticVolumeScalingFactor[score]));
       }
 
-      private Action<string, double> updateBloodFlowDef(Action<IParameter, double, bool> updateParameterFunc, IContainer organism) => (organName, factor) =>
+      private Action<string, double> updateBloodFlowDef(Action<ParameterUpdate> updateParameterFunc, IContainer organism) => (organName, factor) =>
       {
          var parameter = organism.Container(organName).Parameter(SPECIFIC_BLOOD_FLOW_RATE);
-         updateParameterFunc(parameter, factor, true);
+         updateParameterFunc(new(parameter, factor));
       };
 
       private void updateReferenceConcentration(Individual individual, IndividualMolecule individualMolecule, HIFactors factors, int valueOriginId)
       {
          var score = childPughScoreFor(individual);
-         UpdateParameter(valueOriginId)(individualMolecule.ReferenceConcentration, factors[score], true);
+         UpdateParameter(valueOriginId)(new(individualMolecule.ReferenceConcentration, factors[score]));
       }
 
       private double childPughScoreFor(Individual individual) => individual.OriginData.DiseaseStateParameters.FindByName(CHILD_PUGH_SCORE).Value;